Chlamydia Cody’s Portfolio

Preamble

Data

Code

suppressPackageStartupMessages(library(tidyverse))
suppressPackageStartupMessages(library(scales))
library(tidyverse)
library(dplyr)
library(ggplot2)
library(readxl)
library(scales)
library(rnaturalearth)
library(rnaturalearthdata)


Attaching package: 'rnaturalearthdata'

The following object is masked from 'package:rnaturalearth':

    countries110

Code

library(sf)

Linking to GEOS 3.11.0, GDAL 3.5.3, PROJ 9.1.0; sf_use_s2() is TRUE

Code

library(tigris)

To enable caching of data, set `options(tigris_use_cache = TRUE)`
in your R script or .Rprofile.

Code

suppressPackageStartupMessages(library(tigris))

#STIDictionary<-read_excel("STISheet.xlsx")
#knitr::kable(STIDictionary)

Code

data <- read.csv("Chlamydia - Rates of Reported Cases by County United States 2021 .csv")

Visualizations

Code

library(sf)
library(ggplot2)
library(dplyr)
library(ggiraph)

data <- read.csv("Chlamydia - Rates of Reported Cases by County United States 2021 .csv", header = TRUE)
data$Rate <- as.numeric(data$Rate)

Warning: NAs introduced by coercion

Code

invisible({
  us_counties <- tigris::counties(cb = TRUE, resolution = "20m", year = 2020, class = "sf")
})


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Code

us_counties_contiguous <- us_counties %>% 
  filter(
    !(STATEFP %in% c("02", "15", "60", "66", "69", "72", "78"))
  )

us_counties_data <- left_join(us_counties, data, by = c("NAMELSAD" = "County"))

Warning in sf_column %in% names(g): Detected an unexpected many-to-many relationship between `x` and `y`.
ℹ Row 1 of `x` matches multiple rows in `y`.
ℹ Row 65 of `y` matches multiple rows in `x`.
ℹ If a many-to-many relationship is expected, set `relationship =
  "many-to-many"` to silence this warning.

Code

us_counties_data$Rate <- as.numeric(us_counties_data$Rate)

us_counties_data_contiguous <- us_counties_data %>% 
  filter(
    !(STATEFP %in% c("02", "15", "60", "66", "69", "72", "78"))
  )

my_colors <- c('blue', 'purple', 'red', 'orange', 'yellow')


gg <- ggplot() +
  geom_sf_interactive(data = us_counties_data_contiguous, aes(fill = Rate, tooltip = paste(NAMELSAD, "<br>", "Rate:", Rate)), color = "grey", size = 0.1) +
  scale_fill_gradientn(colors = my_colors, na.value = "grey70", name = "Rate") + 
  labs(title = "Chlamydia Infection Rate by County 2021", caption = "Total infection rate by chlamydia by county") +
  theme_minimal() +
  theme(axis.text = element_blank(),
        axis.title = element_blank(),
        axis.ticks = element_blank(),
        panel.grid = element_blank(),
        plot.caption = element_text(hjust = .5, size = 8, margin = margin(t = 10, r = 10)))


ggiraph(code = print(gg))

Function `ggiraph()` is replaced by `girafe()` and will be removed soon.

Code

library(sf)
library(ggplot2)
library(dplyr)
library(ggiraph)

data2 <- read.csv("Gonorrhea - Rates of Reported Cases by County United States 2021 .csv", header = TRUE)
data2$Rate <- as.numeric(data2$Rate)

Warning: NAs introduced by coercion

Code

invisible({
  us_counties <- tigris::counties(cb = TRUE, resolution = "20m", year = 2020, class = "sf")
})

us_counties_contiguous <- us_counties %>% 
  filter(
    !(STATEFP %in% c("02", "15", "60", "66", "69", "72", "78"))
  )

us_counties_data <- left_join(us_counties, data2, by = c("NAMELSAD" = "County"))

Warning in sf_column %in% names(g): Detected an unexpected many-to-many relationship between `x` and `y`.
ℹ Row 1 of `x` matches multiple rows in `y`.
ℹ Row 65 of `y` matches multiple rows in `x`.
ℹ If a many-to-many relationship is expected, set `relationship =
  "many-to-many"` to silence this warning.

Code

us_counties_data$Rate <- as.numeric(us_counties_data$Rate)

us_counties_data_contiguous <- us_counties_data %>% 
  filter(
    !(STATEFP %in% c("02", "15", "60", "66", "69", "72", "78"))
  )

my_colors <- c('blue', 'purple', 'red', 'orange', 'yellow')


gg <- ggplot() +
  geom_sf_interactive(data = us_counties_data_contiguous, aes(fill = Rate, tooltip = paste(NAMELSAD, "<br>", "Rate:", Rate)), color = "grey", size = 0.1) +
  scale_fill_gradientn(colors = my_colors, na.value = "grey70", name = "Rate") + 
  labs(title = "Gonorrhea Infection Rate by County 2021", caption = "Total infection rate by gonorrhea by county") +
  theme_minimal() +
  theme(axis.text = element_blank(),
        axis.title = element_blank(),
        axis.ticks = element_blank(),
        panel.grid = element_blank(),
        plot.caption = element_text(hjust = .5, size = 8, margin = margin(t = 10, r = 10)))


ggiraph(code = print(gg))

Function `ggiraph()` is replaced by `girafe()` and will be removed soon.

Code

library(sf)
library(ggplot2)
library(dplyr)
library(ggiraph)

data3 <- read.csv("Primary and Secondary Syphilis - Rates of Reported Cases by County United States 2021 .csv", header = TRUE)
data3$Rate <- as.numeric(data3$Rate)

Warning: NAs introduced by coercion

Code

invisible({
  us_counties <- tigris::counties(cb = TRUE, resolution = "20m", year = 2020, class = "sf")
})

us_counties_contiguous <- us_counties %>% 
  filter(
    !(STATEFP %in% c("02", "15", "60", "66", "69", "72", "78"))
  )

us_counties_data <- left_join(us_counties, data3, by = c("NAMELSAD" = "County"))

Warning in sf_column %in% names(g): Detected an unexpected many-to-many relationship between `x` and `y`.
ℹ Row 1 of `x` matches multiple rows in `y`.
ℹ Row 65 of `y` matches multiple rows in `x`.
ℹ If a many-to-many relationship is expected, set `relationship =
  "many-to-many"` to silence this warning.

Code

us_counties_data$Rate <- as.numeric(us_counties_data$Rate)

us_counties_data_contiguous <- us_counties_data %>% 
  filter(
    !(STATEFP %in% c("02", "15", "60", "66", "69", "72", "78"))
  )

my_colors <- c('blue', 'purple', 'red', 'orange', 'yellow')


gg <- ggplot() +
  geom_sf_interactive(data = us_counties_data_contiguous, aes(fill = Rate, tooltip = paste(NAMELSAD, "<br>", "Rate:", Rate)), color = "grey", size = 0.1) +
  scale_fill_gradientn(colors = my_colors, na.value = "grey70", name = "Rate") + 
  labs(title = "Primary and Secondary Syphilis Infection Rate by County 2021", caption = "Total infection rate by Primary and Secondary Syphilis by county") +
  theme_minimal() +
  theme(axis.text = element_blank(),
        axis.title = element_blank(),
        axis.ticks = element_blank(),
        panel.grid = element_blank(),
        plot.caption = element_text(hjust = .5, size = 8, margin = margin(t = 10, r = 10)))


ggiraph(code = print(gg))

Function `ggiraph()` is replaced by `girafe()` and will be removed soon.

Final Portfolio

Preamble

Data

Visualizations

Conclusion